 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0073.inter 
CONANA-PAIR            ../CONANA/T0073.pair 
# 
NUMBER-OF-PARENTS      1 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0073.1cos.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff  
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff  
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
# WARNING! TARGET 358 atoms, MODEL 364 atoms, 357 common with TARGET 
           Number of atoms possible to evaluate: 323 
 
 
 CA-RMS TARGET<->PARENT(1cos)	 1.128383 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    31.06           92.9    84    89.4    94     ARMSMC  
     WELL ORDERED  . . . . .    31.06           92.9    84    89.4    94     ARMSMC  
     NO INTER CONTACTS . . .    42.43           83.3    18    94.7    19     ARMSMC  
     SHIFTED CHAIN . . . . .    45.93           83.3    36    78.3    46     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    16.28           98.7    76    92.7    82     ARMSMC  
     LARGE SHIFTS/INSERTIONS    44.99           90.9    11    64.7    17     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    31.90           92.3    78    89.7    87     ARMSMC  
     BURIED  . . . . . . . .    16.69          100.0     6    85.7     7     ARMSMC  
     CORE  . . . . . . . . .    28.38           93.2    73    94.8    77     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    76.46           48.5    33    89.2    37     ARMSSC1 
     WELL ORDERED  . . . . .    76.46           48.5    33    89.2    37     ARMSSC1 
     NO INTER CONTACTS . . .    96.62           33.3     6   100.0     6     ARMSSC1 
     RELIABLE SIDE CHAINS  .    76.46           48.5    33    89.2    37     ARMSSC1 
     CHANGED ANGLES  . . . .    82.85           43.5    23    85.2    27     ARMSSC1 
     SHIFTED CHAIN . . . . .    81.82           46.2    13    76.5    17     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    73.20           50.0    30    93.8    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    82.71           40.0     5    71.4     7     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    80.13           43.3    30    88.2    34     ARMSSC1 
     BURIED  . . . . . . . .     9.51          100.0     3   100.0     3     ARMSSC1 
     CORE  . . . . . . . . .    75.29           50.0    28    93.3    30     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    67.73           48.3    29    90.6    32     ARMSSC2 
     WELL ORDERED  . . . . .    64.42           53.8    26    89.7    29     ARMSSC2 
     NO INTER CONTACTS . . .     8.94          100.0     5   100.0     5     ARMSSC2 
     RELIABLE SIDE CHAINS  .    73.75           52.6    19    95.0    20     ARMSSC2 
     CHANGED ANGLES  . . . .    81.13           37.5    16    84.2    19     ARMSSC2 
     SHIFTED CHAIN . . . . .    83.71           50.0    10    76.9    13     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    61.08           51.9    27    93.1    29     ARMSSC2 
     LARGE SHIFTS/INSERTIONS   100.62            0.0     4    66.7     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    70.78           46.2    26    89.7    29     ARMSSC2 
     BURIED  . . . . . . . .    30.54           66.7     3   100.0     3     ARMSSC2 
     CORE  . . . . . . . . .    60.84           56.0    25    96.2    26     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.89           29.4    17    94.4    18     ARMSSC3 
     WELL ORDERED  . . . . .    80.31           21.4    14    93.3    15     ARMSSC3 
     NO INTER CONTACTS . . .   106.19            0.0     3   100.0     3     ARMSSC3 
     RELIABLE SIDE CHAINS  .    88.99           28.6    14    93.3    15     ARMSSC3 
     CHANGED ANGLES  . . . .    85.11           31.2    16    94.1    17     ARMSSC3 
     SHIFTED CHAIN . . . . .    74.49           57.1     7    87.5     8     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    87.20           25.0    16   100.0    16     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    16.20          100.0     2    66.7     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    84.89           29.4    17    94.4    18     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .    90.18           20.0    15   100.0    15     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    50.83           42.9     7    87.5     8     ARMSSC4 
     WELL ORDERED  . . . . .    41.07           60.0     5   100.0     5     ARMSSC4 
     NO INTER CONTACTS . . .    78.58            0.0     1   100.0     1     ARMSSC4 
     RELIABLE SIDE CHAINS  .    50.83           42.9     7    87.5     8     ARMSSC4 
     CHANGED ANGLES  . . . .    54.88           33.3     6    85.7     7     ARMSSC4 
     SHIFTED CHAIN . . . . .    64.52           25.0     4    80.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    50.83           42.9     7   100.0     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    90.85            0.0     1    50.0     2     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    50.83           42.9     7    87.5     8     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    40.48           50.0     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.60492     r(1,2) =   0.63548     r(1,3) =   0.47982 
 r(2,1) =   0.61900     r(2,2) =  -0.00378     r(2,3) =   0.78538 
 r(3,1) =   0.50091     r(3,2) =   0.77210     r(3,3) =  -0.39108 
THE OFFSET VECTOR: 
 v(1) =  16.35250     v(2) =  34.82939     v(3) =  12.21511 
 
 Number of iteration 28                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.72           (Number of atoms:   25) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.74         43    89.6    48     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2032                            CRMSCA  
     WELL ORDERED  . . . . .    8.74         43    89.6    48     CRMSCA  
     NO INTER CONTACTS . . .    9.38          9    90.0    10     CRMSCA  
     SHIFTED CHAIN . . . . .    9.05         19    79.2    24     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    8.43         39    95.1    41     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.59          6    66.7     9     CRMSCA  
     SURFACE . . . . . . . .    8.85         40    90.9    44     CRMSCA  
     BURIED  . . . . . . . .    7.06          3    75.0     4     CRMSCA  
     CORE  . . . . . . . . .    9.31         37    94.9    39     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.70        213    89.9   237     CRMSMC  
     WELL ORDERED  . . . . .    8.70        213    89.9   237     CRMSMC  
     NO INTER CONTACTS . . .    8.98         44    93.6    47     CRMSMC  
     SHIFTED CHAIN . . . . .    8.98         93    79.5   117     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    8.45        194    94.6   205     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.48         29    67.4    43     CRMSMC  
     SURFACE . . . . . . . .    8.80        198    90.4   219     CRMSMC  
     BURIED  . . . . . . . .    7.25         15    83.3    18     CRMSMC  
     CORE  . . . . . . . . .    9.26        184    94.8   194     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.79        152    91.0   167     CRMSSC  
     WELL ORDERED  . . . . .   10.05        142    91.0   156     CRMSSC  
     NO INTER CONTACTS . . .    5.66         26   100.0    26     CRMSSC  
     RELIABLE SIDE CHAINS  .   10.03        126    92.0   137     CRMSSC  
     CHANGED ANGLES  . . . .   10.50         89    89.0   100     CRMSSC  
     SECONDARY STRUCTURE . .    9.55        138    94.5   146     CRMSSC  
     LARGE SHIFTS/INSERTIONS    5.45         24    72.7    33     CRMSSC  
     SURFACE . . . . . . . .   10.02        140    90.3   155     CRMSSC  
     BURIED  . . . . . . . .    6.56         12   100.0    12     CRMSSC  
     CORE  . . . . . . . . .   10.41        128    95.5   134     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.20        323    90.2   358     CRMSALL 
     WELL ORDERED  . . . . .    9.31        313    90.2   347     CRMSALL 
     NO INTER CONTACTS . . .    7.74         62    95.4    65     CRMSALL 
     SHIFTED CHAIN . . . . .    9.60        136    79.5   171     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    8.94        293    94.5   310     CRMSALL 
     LARGE SHIFTS/INSERTIONS    4.59         47    69.1    68     CRMSALL 
     SURFACE . . . . . . . .    9.36        299    90.3   331     CRMSALL 
     BURIED  . . . . . . . .    6.97         24    88.9    27     CRMSALL 
     CORE  . . . . . . . . .    9.78        276    95.2   290     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.77      5    62.5     8      41-SKLQALKG-48   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.82     24    63.2    38      41-SKLQALKG-48   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.34     36    63.2    57      41-SKLQALKG-48   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.11      5    62.5     8      41-SKLQALKG-48   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.23     24    63.2    38      41-SKLQALKG-48   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.27     36    63.2    57      41-SKLQALKG-48   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.254      0.542       0.389     43    89.6    48     ERRCA  
     WELL ORDERED  . . . . .    5.254      0.542       0.389     43    89.6    48     ERRCA  
     NO INTER CONTACTS . . .    5.960      0.573       0.371      9    90.0    10     ERRCA  
     SHIFTED CHAIN . . . . .    5.461      0.547       0.382     19    79.2    24     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    4.807      0.515       0.387     39    95.1    41     ERRCA  
     LARGE SHIFTS/INSERTIONS    1.601      0.369       0.286      6    66.7     9     ERRCA  
     SURFACE . . . . . . . .    5.355      0.552       0.398     40    90.9    44     ERRCA  
     BURIED  . . . . . . . .    3.910      0.396       0.262      3    75.0     4     ERRCA  
     CORE  . . . . . . . . .    5.846      0.569       0.405     37    94.9    39     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.201      0.542       0.392    213    89.9   237     ERRMC  
     WELL ORDERED  . . . . .    5.201      0.542       0.392    213    89.9   237     ERRMC  
     NO INTER CONTACTS . . .    5.610      0.586       0.401     44    93.6    47     ERRMC  
     SHIFTED CHAIN . . . . .    5.362      0.544       0.385     93    79.5   117     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    4.823      0.519       0.392    194    94.6   205     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.539      0.352       0.283     29    67.4    43     ERRMC  
     SURFACE . . . . . . . .    5.289      0.552       0.400    198    90.4   219     ERRMC  
     BURIED  . . . . . . . .    4.037      0.411       0.283     15    83.3    18     ERRMC  
     CORE  . . . . . . . . .    5.778      0.572       0.409    184    94.8   194     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.257      0.560       0.311    152    91.0   167     ERRSC  
     WELL ORDERED  . . . . .    6.457      0.558       0.313    142    91.0   156     ERRSC  
     NO INTER CONTACTS . . .    2.729      0.408       0.233     26   100.0    26     ERRSC  
     RELIABLE SIDE CHAINS  .    6.509      0.576       0.326    126    92.0   137     ERRSC  
     CHANGED ANGLES  . . . .    7.124      0.609       0.309     89    89.0   100     ERRSC  
     SHIFTED CHAIN . . . . .    6.538      0.570       0.324     61    80.3    76     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    5.882      0.535       0.302    138    94.5   146     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.552      0.525       0.300     24    72.7    33     ERRSC  
     SURFACE . . . . . . . .    6.486      0.577       0.321    140    90.3   155     ERRSC  
     BURIED  . . . . . . . .    3.584      0.358       0.192     12   100.0    12     ERRSC  
     CORE  . . . . . . . . .    6.764      0.566       0.313    128    95.5   134     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.695      0.555       0.359    323    90.2   358     ERRALL 
     WELL ORDERED  . . . . .    5.768      0.554       0.361    313    90.2   347     ERRALL 
     NO INTER CONTACTS . . .    4.442      0.521       0.337     62    95.4    65     ERRALL 
     SHIFTED CHAIN . . . . .    5.917      0.561       0.359    136    79.5   171     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    5.297      0.530       0.355    293    94.5   310     ERRALL 
     LARGE SHIFTS/INSERTIONS    2.569      0.444       0.290     47    69.1    68     ERRALL 
     SURFACE . . . . . . . .    5.843      0.568       0.368    299    90.3   331     ERRALL 
     BURIED  . . . . . . . .    3.854      0.390       0.244     24    88.9    27     ERRALL 
     CORE  . . . . . . . . .    6.228      0.574       0.371    276    95.2   290     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)        22        25        25        26        29      43      48   DISTCA 
CA  (P)     45.83     52.08     52.08     54.17     60.42              48   DISTCA 
CA  (RMS)    0.54      0.72      0.72      1.17      2.40                   DISTCA 
 
ALL (N)       120       150       168       188       218     323     358   DISTALL 
ALL (P)     33.52     41.90     46.93     52.51     60.89             358   DISTALL 
ALL (RMS)    0.57      0.82      1.13      1.66      3.08                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)          39            37             6          RMSLSI 
CA  (P)       81.25         77.08         12.50          RMSLSI 
CA  (RMS)      1.02          9.31          3.59          RMSLSI 
 
 
 
END of the results output 
